diff --git a/Inst_eddies/Analysis/eddy_dump.py b/Inst_eddies/Analysis/eddy_dump.py
index 238184824f9f76dee5e2acfc3e2803e83961d1cb..bca355615243bc675ee8045bd861ce8ce2a9c55e 100755
--- a/Inst_eddies/Analysis/eddy_dump.py
+++ b/Inst_eddies/Analysis/eddy_dump.py
@@ -16,21 +16,21 @@ import shapefile
import util_eddies
parser = argparse.ArgumentParser()
-parser.add_argument("directory", metavar = "SHPC-directory")
-parser.add_argument("orientation", choices = ["Anticyclones", "Cyclones"])
+parser.add_argument("directory", metavar="SHPC-directory")
+parser.add_argument("orientation", choices=["Anticyclones", "Cyclones"])
group = parser.add_mutually_exclusive_group()
-group.add_argument("-i", "--ishape", type = int)
-group.add_argument("-n", "--node", type = int)
+group.add_argument("-i", "--ishape", type=int)
+group.add_argument("-n", "--node", type=int)
args = parser.parse_args()
-SHPC = util_eddies.SHPC_class(args.directory, def_orient = args.orientation)
+SHPC = util_eddies.SHPC_class(args.directory, def_orient=args.orientation)
if args.ishape:
ishape = args.ishape
else:
if args.node:
- with open("e_overestim.txt") as f: e_overestim = int(f.read())
- date, eddy_index = util_eddies.node_to_date_eddy(args.node,
- e_overestim)
+ with open("e_overestim.txt") as f:
+ e_overestim = int(f.read())
+ date, eddy_index = util_eddies.node_to_date_eddy(args.node, e_overestim)
else:
reply = input("date, eddy_index = ? ").split(",")
date = int(reply[0])
@@ -45,8 +45,9 @@ for layer in ["extremum", "outermost_contour", "max_speed_contour", "centroid"]:
print()
try:
- shapeRec = SHPC.get_reader(0, args.orientation, layer)\
- .shapeRecord(ishape)
+ shapeRec = SHPC.get_reader(0, args.orientation, layer).shapeRecord(
+ ishape
+ )
except AttributeError:
pass
else:
diff --git a/Overlap/report_graph.py b/Overlap/report_graph.py
index 49d1925c0505e0efef649c45eeb66b730fd2f8ad..a5ddb666c77b6e43703a8365e5ad177150fc6974 100755
--- a/Overlap/report_graph.py
+++ b/Overlap/report_graph.py
@@ -8,13 +8,14 @@ import os
import json
import util_eddies
-def read_eddy_graph(edgelist, shpc_dir = None, orientation = "Cyclones"):
+
+def read_eddy_graph(edgelist, shpc_dir=None, orientation="Cyclones"):
if os.access(edgelist, os.R_OK):
- G = nx.read_edgelist(edgelist, create_using = nx.DiGraph,
- nodetype = int)
+ G = nx.read_edgelist(edgelist, create_using=nx.DiGraph, nodetype=int)
dir_edgelist = path.dirname(edgelist)
e_overestim_file = path.join(dir_edgelist, "e_overestim.txt")
- with open(e_overestim_file) as f: G.graph["e_overestim"] = int(f.read())
+ with open(e_overestim_file) as f:
+ G.graph["e_overestim"] = int(f.read())
if shpc_dir is not None:
# Read and set attributes of eddies:
@@ -26,28 +27,39 @@ def read_eddy_graph(edgelist, shpc_dir = None, orientation = "Cyclones"):
return G
+
def set_attribute(G, SHPC, orientation):
reader = SHPC.get_reader(0, orientation, "extremum")
if G.number_of_nodes() <= SHPC.get_n_shapes(0, orientation) / 100:
for n in G:
- date_index, eddy_index = util_eddies.node_to_date_eddy(n,
- G.graph["e_overestim"])
+ date_index, eddy_index = util_eddies.node_to_date_eddy(
+ n, G.graph["e_overestim"]
+ )
ishape = SHPC.comp_ishape(date_index, eddy_index, 0, orientation)
shape_rec = reader.shapeRecord(ishape)
- G.add_node(n, coordinates = tuple(shape_rec.shape.points[0]),
- speed = shape_rec.record.speed,
- ssh = shape_rec.record.ssh)
+ G.add_node(
+ n,
+ coordinates=tuple(shape_rec.shape.points[0]),
+ speed=shape_rec.record.speed,
+ ssh=shape_rec.record.ssh,
+ )
else:
for shape_rec in reader:
- n = util_eddies.date_eddy_to_node(shape_rec.record.date,
- shape_rec.record.eddy_index,
- G.graph["e_overestim"])
+ n = util_eddies.date_eddy_to_node(
+ shape_rec.record.date,
+ shape_rec.record.eddy_index,
+ G.graph["e_overestim"],
+ )
if n in G:
- G.add_node(n, coordinates = tuple(shape_rec.shape.points[0]),
- speed = shape_rec.record.speed,
- ssh = shape_rec.record.ssh)
+ G.add_node(
+ n,
+ coordinates=tuple(shape_rec.shape.points[0]),
+ speed=shape_rec.record.speed,
+ ssh=shape_rec.record.ssh,
+ )
+
def partition_graph_date(A, e_overestim):
"""Add subgraphs in pygraphviz graph, one subgraph for each date. We
@@ -59,7 +71,9 @@ def partition_graph_date(A, e_overestim):
my_subgraphs = {}
for n in A.iternodes():
- date_index = util_eddies.node_to_date_eddy(int(n), e_overestim, only_date = True)
+ date_index = util_eddies.node_to_date_eddy(
+ int(n), e_overestim, only_date=True
+ )
if date_index in my_subgraphs:
my_subgraphs[date_index].append(n)
@@ -67,7 +81,8 @@ def partition_graph_date(A, e_overestim):
my_subgraphs[date_index] = [n]
for date, s in my_subgraphs.items():
- A.add_subgraph(s, rank = "same")
+ A.add_subgraph(s, rank="same")
+
def add_component(G: nx.DiGraph, source: int):
"""Add the weakly-connected component containing node source.
@@ -89,7 +104,9 @@ def add_component(G: nx.DiGraph, source: int):
else:
G.graph["component_list"] = [component]
- for n in component: G.nodes[n]["component"] = component
+ for n in component:
+ G.nodes[n]["component"] = component
+
if __name__ == "__main__":
import argparse
@@ -97,13 +114,18 @@ if __name__ == "__main__":
# Parse arguments:
parser = argparse.ArgumentParser()
parser.add_argument("edgelist_file")
- parser.add_argument("--gv", help = "Create Graphviz file",
- action = "store_true")
- parser.add_argument("-n", "--node",
- help = "Select component containing node", type = int)
- parser.add_argument("-m", "--merging",
- help = "Report merging and splitting events",
- action = "store_true")
+ parser.add_argument(
+ "--gv", help="Create Graphviz file", action="store_true"
+ )
+ parser.add_argument(
+ "-n", "--node", help="Select component containing node", type=int
+ )
+ parser.add_argument(
+ "-m",
+ "--merging",
+ help="Report merging and splitting events",
+ action="store_true",
+ )
args = parser.parse_args()
G = read_eddy_graph(args.edgelist_file)
@@ -116,23 +138,29 @@ if __name__ == "__main__":
len_H = len(H)
print("Number of nodes:", len_H)
- print("(This should be the number of eddies minus the number of isolated "
- "nodes.)")
+ print(
+ "(This should be the number of eddies minus the number of isolated "
+ "nodes.)"
+ )
print("Number of edges:", H.number_of_edges())
- print("Number of weakly connected components:",
- nx.number_weakly_connected_components(H))
+ print(
+ "Number of weakly connected components:",
+ nx.number_weakly_connected_components(H),
+ )
n1 = len_H
n2 = len_H
if len_H >= 1:
# First and last dates:
node_index = min(G.nodes)
- my_date = util_eddies.node_to_date_eddy(node_index, G.graph["e_overestim"],
- only_date = True)
+ my_date = util_eddies.node_to_date_eddy(
+ node_index, G.graph["e_overestim"], only_date=True
+ )
print("First date:", my_date)
node_index = max(G.nodes)
- my_date = util_eddies.node_to_date_eddy(node_index, G.graph["e_overestim"],
- only_date = True)
+ my_date = util_eddies.node_to_date_eddy(
+ node_index, G.graph["e_overestim"], only_date=True
+ )
print("Last date:", my_date)
if args.merging:
@@ -141,7 +169,8 @@ if __name__ == "__main__":
for n, d in H.in_degree():
if d >= 1:
n2 -= 1
- if args.merging and d >= 2: print(list(H.predecessors(n)), "->", n)
+ if args.merging and d >= 2:
+ print(list(H.predecessors(n)), "->", n)
if args.merging:
print("---")
@@ -150,7 +179,8 @@ if __name__ == "__main__":
for n, d in H.out_degree():
if d >= 1:
n1 -= 1
- if args.merging and d >= 2: print(n, "->", list(H.successors(n)))
+ if args.merging and d >= 2:
+ print(n, "->", list(H.successors(n)))
if args.merging:
print("---")
diff --git a/Trajectories/draw_segments.py b/Trajectories/draw_segments.py
index fc4701f54f97877eb02448c82dd9eb211000db7d..1be68917e4c60938c127ec90fd4039702762bc01 100755
--- a/Trajectories/draw_segments.py
+++ b/Trajectories/draw_segments.py
@@ -19,15 +19,17 @@ import report_graph
import util_eddies
parser = argparse.ArgumentParser()
-parser.add_argument("input_file", help = "Graph-tool file")
-parser.add_argument("output_file", help = "Graphviz file")
-parser.add_argument("-t",
- help = "trajectories as lists of segments, JSON file, to "
- "label each segment with trajectory")
+parser.add_argument("input_file", help="Graph-tool file")
+parser.add_argument("output_file", help="Graphviz file")
+parser.add_argument(
+ "-t",
+ help="trajectories as lists of segments, JSON file, to "
+ "label each segment with trajectory",
+)
args = parser.parse_args()
g_in = graph_tool.load_graph(args.input_file)
-g_out = pgv.AGraph(directed = True)
+g_out = pgv.AGraph(directed=True)
for v in g_in.vertices():
g_out.add_node(g_in.vp.name[v])
@@ -35,18 +37,34 @@ for v in g_in.vertices():
report_graph.partition_graph_date(g_out, g_in.gp.e_overestim)
for e in g_in.edges():
- source = e.source()
+ source = e.source()
target = e.target()
try:
- g_out.add_edge(g_in.vp.name[source], g_in.vp.name[target],
- label = f"{g_in.ep.cost_function[e]:.2g}")
+ g_out.add_edge(
+ g_in.vp.name[source],
+ g_in.vp.name[target],
+ label=f"{g_in.ep.cost_function[e]:.2g}",
+ )
except AttributeError:
g_out.add_edge(g_in.vp.name[source], g_in.vp.name[target])
if args.t:
- with open(args.t) as f: traj_segm = json.load(f)
- colors = itertools.cycle(['blue', 'orange', 'green', 'red', 'purple',
- 'brown', 'pink', 'gray', 'olive', 'cyan'])
+ with open(args.t) as f:
+ traj_segm = json.load(f)
+ colors = itertools.cycle(
+ [
+ "blue",
+ "orange",
+ "green",
+ "red",
+ "purple",
+ "brown",
+ "pink",
+ "gray",
+ "olive",
+ "cyan",
+ ]
+ )
for i, segment_list in enumerate(traj_segm):
color = next(colors)
@@ -57,17 +75,17 @@ if args.t:
except KeyError:
break
else:
- date_index = util_eddies.node_to_date_eddy(segment,
- g_in.gp.e_overestim,
- only_date = True)
+ date_index = util_eddies.node_to_date_eddy(
+ segment, g_in.gp.e_overestim, only_date=True
+ )
n.attr["label"] = f"{segment} in {i}\n({date_index})"
n.attr["color"] = color
else:
for n in g_out.iternodes():
segment = int(n)
- date_index = util_eddies.node_to_date_eddy(segment,
- g_in.gp.e_overestim,
- only_date = True)
+ date_index = util_eddies.node_to_date_eddy(
+ segment, g_in.gp.e_overestim, only_date=True
+ )
n.attr["label"] = f"{segment}\n({date_index})"
g_out.write(args.output_file)
diff --git a/Trajectories/filter_traj.py b/Trajectories/filter_traj.py
index 354ed35791906fdfc4b723e8d24bcfac1cf61cb7..7fcbdb198df64887c9e6ab2a3da28a7cdec0f2d2 100755
--- a/Trajectories/filter_traj.py
+++ b/Trajectories/filter_traj.py
@@ -9,15 +9,19 @@ if len(sys.argv) != 4:
sys.exit("Required arguments: last-date input-file output-file")
last_date = int(sys.argv[1])
-with open(sys.argv[2]) as f: expanded_traj = json.load(f)
+with open(sys.argv[2]) as f:
+ expanded_traj = json.load(f)
last_node = util_eddies.date_eddy_to_node(
- last_date, expanded_traj["e_overestim"], expanded_traj["e_overestim"])
+ last_date, expanded_traj["e_overestim"], expanded_traj["e_overestim"]
+)
filt_traj = []
for t in expanded_traj["traj"]:
ip = bisect.bisect(t, last_node)
- if ip != 0: filt_traj.append(t[:ip])
+ if ip != 0:
+ filt_traj.append(t[:ip])
with open(sys.argv[3], "w") as f:
- json.dump({"e_overestim": expanded_traj["e_overestim"], "traj": filt_traj},
- f)
+ json.dump(
+ {"e_overestim": expanded_traj["e_overestim"], "traj": filt_traj}, f
+ )
diff --git a/Trajectories/plot_traj.py b/Trajectories/plot_traj.py
index 76368d949911e17e8ace3544fa69742bbdbea89b..85842cc102ea0e516d9e28d2d0eba19cbf857ebc 100755
--- a/Trajectories/plot_traj.py
+++ b/Trajectories/plot_traj.py
@@ -4,6 +4,7 @@ import util_eddies
import random
import numpy as np
+
def get_extr_coord(traj, e_overestim, SHPC, orientation):
"""Get the coordinates of the extrema of instantaneous eddies along a
given trajectory.
@@ -14,42 +15,53 @@ def get_extr_coord(traj, e_overestim, SHPC, orientation):
y = []
for node in traj:
- date_index, eddy_index = util_eddies.node_to_date_eddy(node,
- e_overestim)
+ date_index, eddy_index = util_eddies.node_to_date_eddy(
+ node, e_overestim
+ )
i_slice = SHPC.get_slice(date_index)
ishape = SHPC.comp_ishape(date_index, eddy_index, i_slice, orientation)
- shape = SHPC.get_reader(i_slice, orientation, layer = "extremum")\
- .shape(ishape)
+ shape = SHPC.get_reader(i_slice, orientation, layer="extremum").shape(
+ ishape
+ )
x.append(shape.points[0][0])
y.append(shape.points[0][1])
return x, y
-def plot_single_traj(traj, e_overestim, SHPC, orientation, ax, src_crs,
- annotate_flag, color):
+
+def plot_single_traj(
+ traj, e_overestim, SHPC, orientation, ax, src_crs, annotate_flag, color
+):
x, y = get_extr_coord(traj, e_overestim, SHPC, orientation)
- ax.plot(x, y, color, linewidth = 0.5, transform = src_crs)
- ax.plot(x[0], y[0], marker = "s", markersize = 2, color = "green",
- transform = src_crs)
+ ax.plot(x, y, color, linewidth=0.5, transform=src_crs)
+ ax.plot(
+ x[0], y[0], marker="s", markersize=2, color="green", transform=src_crs
+ )
if annotate_flag:
- ax.annotate(str(traj[0]),
- ax.projection.transform_point(x[0], y[0], src_crs),
- xytext = (3 * random.random(), 3 * random.random()),
- textcoords = "offset points")
+ ax.annotate(
+ str(traj[0]),
+ ax.projection.transform_point(x[0], y[0], src_crs),
+ xytext=(3 * random.random(), 3 * random.random()),
+ textcoords="offset points",
+ )
+
def get_duration(expanded_traj):
duration_list = []
for traj in expanded_traj["traj"]:
init_date = util_eddies.node_to_date_eddy(
- traj[0], expanded_traj["e_overestim"], only_date = True)
+ traj[0], expanded_traj["e_overestim"], only_date=True
+ )
final_date = util_eddies.node_to_date_eddy(
- traj[- 1], expanded_traj["e_overestim"], only_date = True)
+ traj[-1], expanded_traj["e_overestim"], only_date=True
+ )
duration_list.append(final_date - init_date)
return np.array(duration_list)
+
if __name__ == "__main__":
import util_eddies
import matplotlib.pyplot as plt
@@ -59,30 +71,48 @@ if __name__ == "__main__":
import cartopy.feature as cfeature
parser = argparse.ArgumentParser()
- parser.add_argument("expanded_traj", help = "JSon file")
- parser.add_argument("SHPC", help = "directory")
- parser.add_argument("--save", metavar = "format",
- help = "Save file to specified format")
- parser.add_argument("--annotate", action = "store_true", help = "annotate "
- "the first point of trajectory with node number")
- parser.add_argument("--min_duration", type = int, default = 1,
- help = "minimum duration of plotted trajectories (in "
- "time steps), >= 1")
+ parser.add_argument("expanded_traj", help="JSon file")
+ parser.add_argument("SHPC", help="directory")
+ parser.add_argument(
+ "--save", metavar="format", help="Save file to specified format"
+ )
+ parser.add_argument(
+ "--annotate",
+ action="store_true",
+ help="annotate " "the first point of trajectory with node number",
+ )
+ parser.add_argument(
+ "--min_duration",
+ type=int,
+ default=1,
+ help="minimum duration of plotted trajectories (in "
+ "time steps), >= 1",
+ )
args = parser.parse_args()
- with open(args.expanded_traj) as f: expanded_traj = json.load(f)
+ with open(args.expanded_traj) as f:
+ expanded_traj = json.load(f)
print("Number of trajectories:", len(expanded_traj["traj"]))
- SHPC = util_eddies.SHPC_class(args.SHPC, def_orient = expanded_traj["orientation"])
+ SHPC = util_eddies.SHPC_class(
+ args.SHPC, def_orient=expanded_traj["orientation"]
+ )
src_crs = ccrs.Geodetic()
- projection = ccrs.Mercator(central_longitude = 110)
- fig, ax = plt.subplots(subplot_kw = {"projection": projection})
+ projection = ccrs.Mercator(central_longitude=110)
+ fig, ax = plt.subplots(subplot_kw={"projection": projection})
random.seed(0)
if args.min_duration == 1:
for traj in expanded_traj["traj"]:
plot_single_traj(
- traj, expanded_traj["e_overestim"], SHPC, expanded_traj["orientation"], ax,
- src_crs, args.annotate, color = "red")
+ traj,
+ expanded_traj["e_overestim"],
+ SHPC,
+ expanded_traj["orientation"],
+ ax,
+ src_crs,
+ args.annotate,
+ color="red",
+ )
else:
# args.min_duration > 1
n_long_traj = 0
@@ -92,16 +122,25 @@ if __name__ == "__main__":
if duration >= args.min_duration:
n_long_traj += 1
plot_single_traj(
- traj, expanded_traj["e_overestim"], SHPC, expanded_traj["orientation"],
- ax, src_crs, args.annotate, color = "red")
+ traj,
+ expanded_traj["e_overestim"],
+ SHPC,
+ expanded_traj["orientation"],
+ ax,
+ src_crs,
+ args.annotate,
+ color="red",
+ )
print("Number of trajectories with sufficient duration:", n_long_traj)
- ax.set_title(rf"lifetime $\geq$ {args.min_duration} time steps"
- f"\nnumber of trajectories: {n_long_traj}")
-
- ax.set_title(expanded_traj["orientation"], loc = "left")
- ax.add_feature(cfeature.LAND, edgecolor = "black")
- ax.gridlines(draw_labels = True)
+ ax.set_title(
+ rf"lifetime $\geq$ {args.min_duration} time steps"
+ f"\nnumber of trajectories: {n_long_traj}"
+ )
+
+ ax.set_title(expanded_traj["orientation"], loc="left")
+ ax.add_feature(cfeature.LAND, edgecolor="black")
+ ax.gridlines(draw_labels=True)
if args.save:
plt.savefig(f"plot_traj.{args.save}")
diff --git a/Trajectories/trajectories.py b/Trajectories/trajectories.py
index bfc2a1e8a64898d17d1b843b5aef1d06962fbd39..35e7cf5578198827a5a1ff5dca67806292f8ebb2 100755
--- a/Trajectories/trajectories.py
+++ b/Trajectories/trajectories.py
@@ -20,6 +20,7 @@ import util_eddies
import numpy as np
import time
+
def new_traj(ind_traj, traj_prop, n, traj_vert_ind):
"""Assign new trajectory to vertex index n."""
@@ -28,9 +29,11 @@ def new_traj(ind_traj, traj_prop, n, traj_vert_ind):
traj_vert_ind.append([n])
return ind_traj
+
t0 = time.perf_counter()
timings_file = open("timings.txt", "w")
-if len(sys.argv) != 2: sys.exit("Required argument: input-graph")
+if len(sys.argv) != 2:
+ sys.exit("Required argument: input-graph")
g = graph_tool.load_graph(sys.argv[1])
print("Input graph:")
print("Number of vertices:", g.num_vertices())
@@ -38,22 +41,22 @@ print("Number of edges:", g.num_edges())
print("Internal properties:")
g.list_properties()
t1 = time.perf_counter()
-timings_file.write(f'Loading done in {t1 - t0:.0f} s\n')
+timings_file.write(f"Loading done in {t1 - t0:.0f} s\n")
t0 = t1
if "cost_function" in g.edge_properties:
- closest_succ = g.new_vertex_property('int')
+ closest_succ = g.new_vertex_property("int")
# Index of the closest direct successor of a node: tail of the
# out-edge with smallest cost. - 1 means there is no successor.
# Set closest_succ for all nodes:
for n in g.iter_vertices():
- all_cost = g.get_out_edges(n, eprops = [g.ep.cost_function])
+ all_cost = g.get_out_edges(n, eprops=[g.ep.cost_function])
# numpy array with dtype float64
if all_cost.size == 0:
# n has no successor
- closest_succ[n] = - 1
+ closest_succ[n] = -1
else:
i_min = all_cost[:, 2].argmin()
closest_succ[n] = all_cost[i_min, 1]
@@ -62,14 +65,14 @@ else:
print("No cost values in the input file.")
t1 = time.perf_counter()
-timings_file.write(f'closest_succ defined in {t1 - t0:.0f} s\n')
+timings_file.write(f"closest_succ defined in {t1 - t0:.0f} s\n")
t0 = t1
-traj_prop = g.new_vertex_property('int', val = - 1)
+traj_prop = g.new_vertex_property("int", val=-1)
# Trajectory index to which a segment belongs. - 1 means the segment
# does not belong yet to any trajectory. The trajectory index is also
# the index in lists traj_vert_ind, traj_segm and expanded_traj.
-ind_traj = - 1 # initialize index of trajectory
+ind_traj = -1 # initialize index of trajectory
traj_vert_ind = []
# An element of traj_vert_ind is a trajectory, represented by a list
@@ -89,8 +92,13 @@ for n in topology.topological_sort(g):
if in_deg_prop[n] == 2:
pred = g.get_in_neighbors(n)
- if in_deg_prop[pred[0]] == 1 == in_deg_prop[pred[1]] \
- == out_deg_prop[pred[0]] == out_deg_prop[pred[1]]:
+ if (
+ in_deg_prop[pred[0]]
+ == 1
+ == in_deg_prop[pred[1]]
+ == out_deg_prop[pred[0]]
+ == out_deg_prop[pred[1]]
+ ):
n1 = g.get_in_neighbors(pred[0])[0]
n2 = g.get_in_neighbors(pred[1])[0]
@@ -102,18 +110,21 @@ for n in topology.topological_sort(g):
# splitting is the date of the last eddy in segment
# n1.
date_merging = util_eddies.node_to_date_eddy(
- g.vp.name[n], g.gp.e_overestim, only_date = True)
+ g.vp.name[n], g.gp.e_overestim, only_date=True
+ )
date_splitting = util_eddies.node_to_date_eddy(
- g.vp.inst_eddies[n1][- 1], g.gp.e_overestim,
- only_date = True)
+ g.vp.inst_eddies[n1][-1], g.gp.e_overestim, only_date=True
+ )
if date_merging - date_splitting <= 6:
# We have a phantom pattern. Get the vertex on the
# side of the shortest path:
- if g.ep.cost_function[(n1, pred[0])] \
- + g.ep.cost_function[(pred[0], n)] \
- < g.ep.cost_function[(n1, pred[1])] \
- + g.ep.cost_function[(pred[1], n)]:
+ if (
+ g.ep.cost_function[(n1, pred[0])]
+ + g.ep.cost_function[(pred[0], n)]
+ < g.ep.cost_function[(n1, pred[1])]
+ + g.ep.cost_function[(pred[1], n)]
+ ):
v_short = pred[0]
else:
v_short = pred[1]
@@ -123,22 +134,27 @@ for n in topology.topological_sort(g):
# according to closest successor, that is:
# swap the trajectories of pred[0] and
# pred[1]:
- traj_prop[pred[0]], traj_prop[pred[1]] \
- = traj_prop[pred[1]], traj_prop[pred[0]]
- traj_vert_ind[traj_prop[pred[0]]][- 1], \
- traj_vert_ind[traj_prop[pred[1]]][- 1] \
- = traj_vert_ind[traj_prop[pred[1]]][- 1], \
- traj_vert_ind[traj_prop[pred[0]]][- 1]
+ traj_prop[pred[0]], traj_prop[pred[1]] = (
+ traj_prop[pred[1]],
+ traj_prop[pred[0]],
+ )
+ (
+ traj_vert_ind[traj_prop[pred[0]]][-1],
+ traj_vert_ind[traj_prop[pred[1]]][-1],
+ ) = (
+ traj_vert_ind[traj_prop[pred[1]]][-1],
+ traj_vert_ind[traj_prop[pred[0]]][-1],
+ )
traj_prop[n] = traj_prop[n1]
traj_vert_ind[traj_prop[n1]].append(n)
- if traj_prop[n] == - 1:
+ if traj_prop[n] == -1:
if in_deg_prop[n] >= 1:
# Find the index of the closest direct predecessor of a node:
# head of the in-edge with smallest cost.
- all_cost = g.get_in_edges(n, eprops = [g.ep.cost_function])
+ all_cost = g.get_in_edges(n, eprops=[g.ep.cost_function])
# numpy array with dtype float64
i_min = all_cost[:, 2].argmin()
@@ -160,7 +176,7 @@ for n in topology.topological_sort(g):
# traj_prop[n] != - 1
t1 = time.perf_counter()
-timings_file.write(f'traj_prop defined in {t1 - t0:.0f} s\n')
+timings_file.write(f"traj_prop defined in {t1 - t0:.0f} s\n")
t0 = t1
print("Number of trajectories: ", len(traj_vert_ind))
@@ -177,8 +193,8 @@ expanded_traj = []
for t in traj_vert_ind:
# t is a trajectory as a list of vertex indices.
- list_segm = [] # list of segments in trajectory t
- list_eddies_traj = [] # list of eddies in trajectory t
+ list_segm = [] # list of segments in trajectory t
+ list_eddies_traj = [] # list of eddies in trajectory t
for n in t:
list_segm.append(g.vp.name[n])
@@ -192,22 +208,28 @@ for t in traj_vert_ind:
expanded_traj.append(list_eddies_traj)
t1 = time.perf_counter()
-timings_file.write(f'traj_segm and expanded_traj defined in {t1 - t0:.0f} s\n')
+timings_file.write(f"traj_segm and expanded_traj defined in {t1 - t0:.0f} s\n")
t0 = t1
# Save:
with open("traj_segm.json", "w") as outfile:
- json.dump(traj_segm, outfile, separators = (',', ':'))
+ json.dump(traj_segm, outfile, separators=(",", ":"))
print("Created traj_segm.json.")
with open("expanded_traj.json", "w") as outfile:
- json.dump({"orientation": g.gp.orientation,
- "e_overestim": g.gp.e_overestim, "traj": expanded_traj},
- outfile, separators = (',', ':'))
+ json.dump(
+ {
+ "orientation": g.gp.orientation,
+ "e_overestim": g.gp.e_overestim,
+ "traj": expanded_traj,
+ },
+ outfile,
+ separators=(",", ":"),
+ )
print("Created expanded_traj.json.")
t1 = time.perf_counter()
-timings_file.write(f'Saving done in {t1 - t0:.0f} s\n')
-print('Done')
+timings_file.write(f"Saving done in {t1 - t0:.0f} s\n")
+print("Done")